My experience with upgrading versions in abantecart shows it's pretty important that these permissions are set to specifications. I've not have any issues upgrading when there are set correctly.
Here's the link for docs with the list
http://www.abantecart.com/ecommerce-documentation/user-manual/installation (http://www.abantecart.com/ecommerce-documentation/user-manual/installationhttp://)
For Linux/Unix make sure the following folders and files are writable.
chmod 0777 system/config.php chmod 0777 system/ chmod 0777 system/cache/ chmod 0777 system/logs/ chmod 0777 image/ chmod 0777 image/thumbnails/ chmod 0777 download/ chmod 0777 extensions/ chmod 0777 admin/system/backup/
Here's a link to a nice little how-to on changing file permissions using Cpanel
http://www.inmotionhosting.com/support/website/managing-files/change-file-permissions (http://www.inmotionhosting.com/support/website/managing-files/change-file-permissions)
Lee